One problem related to clutch pedal/linkage has been reported for the 2000 Honda Civic. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2000 Honda Civic based on all problems reported for the 2000 Civic.
Noise from transmission area. Noise when gas pedal is released, in gears 5,4,3, and maybe 2 &1 but rpm's too high to hear. Happens only in gear and only when the clutch is engaged. Local dealer, stevens creek Honda have replaced throw-out bearing & gear bearings with no relief.